Emory 8
Overview:
This page contains the results of CoNGA analyses.
Results in tables may have been filtered to reduce redundancy,
focus on the most important columns, and
limit length; full tables should exist as OUTFILE_PREFIX*.tsv files.
Command:
scripts/run_conga.py --all --gex_data /scratch.global/ben_testing/ben_tcr/Pair_8_Emory/outs/filtered_feature_bc_matrix.h5 --gex_data_type 10x_h5 --clones_file emoryPair8Final.tsv --organism human --outfile_prefix emoryPair8Final
Stats
num_cells_w_gex: 13705
num_features_start: 26530
num_cells_w_tcr: 1227
min_genes_per_cell: 200
max_genes_per_cell: 3500
max_percent_mito: 0.1
num_filt_max_genes_per_cell: 912
num_filt_max_percent_mito: 0
num_antibody_features: 0
num_TR_genes: 43
num_TR_genes_in_hvg_set: 38
num_highly_variable_genes: 2269
num_cells_after_filtering: 315
num_clonotypes: 262
max_clonotype_size: 12
num_singleton_clonotypes: 236
nbr_frac_for_nndists: 0.1
num_gvg_hit_clonotypes: 6
num_gvg_hit_biclusters: 0
graph_vs_graph_stats
Here we are assessing overall graph-vs-graph correlation by looking at
the shared edges between TCR and GEX neighbor graphs and comparing
that observed number to the number we would expect if the graphs were
completely uncorrelated. Our null model for uncorrelated graphs is to
take the vertices of one graph and randomly renumber them (permute their
labels). We compare the observed overlap to that expected under this null
model by computing a Z-score, either by permuting one of the graph's
vertices many times to get a mean and standard deviation of the overlap
distribution, or, for large graphs where this is time consuming,
by using a regression model for the
standard deviation. The different rows of this table correspond to the
different graph-graph comparisons that we make in the conga graph-vs-graph
analysis: we compare K-nearest-neighbor graphs for GEX and TCR at different
K values ("nbr_frac" aka neighbor-fraction, which reports K as a fraction
of the total number of clonotypes) to each other and to GEX and TCR "cluster"
graphs in which each clonotype is connected to all the other clonotypes with
the same (GEX or TCR) cluster assignment. For two K values (the default),
this gives 2*3=6 comparisons: GEX KNN graph vs TCR KNN graph, GEX cluster
graph vs TCR KNN graph, and GEX KNN graph vs TCR cluster graph, for each of the
two K values (aka nbr_fracs).
The column to look at is *overlap_zscore*. Higher values indicate more
significant GEX/TCR covariation, with "interesting" levels starting around
zscores of 3-5.
Columns in more detail:
graph_overlap_type: KNN ("nbr") or cluster versus KNN ("nbr") or cluster
nbr_frac: the K value for the KNN graph, as a fraction of total clonotypes
overlap: the observed overlap (number of shared edges) between GEX and TCR
graphs
expected_overlap: the expected overlap under a shuffled null model.
overlap_zscore: a Z-score for the observed overlap computed by subtracting
the expected overlap and dividing by the standard deviation estimated from
shuffling.
| overlap |
expected_overlap |
overlap_mean |
overlap_sdev |
overlap_zscore |
overlap_zscore_fitted |
overlap_zscore_source |
nodes |
calculation_time |
calculation_time_fitted |
gex_edges |
tcr_edges |
gex_indegree_variance |
gex_indegree_skewness |
gex_indegree_kurtosis |
tcr_indegree_variance |
tcr_indegree_skewness |
tcr_indegree_kurtosis |
indegree_correlation_R |
indegree_correlation_P |
nbr_frac |
graph_overlap_type |
| 2 |
4.015326 |
4.09 |
2.020371 |
-1.034463 |
-1.694141 |
shuffling |
262 |
0.050308 |
0.000231 |
524 |
524 |
1.643678 |
2.098540 |
5.672902 |
0.597701 |
0.878505 |
0.883814 |
0.035756 |
0.564493 |
0.01 |
gex_nbr_vs_tcr_nbr |
| 94 |
84.659004 |
84.25 |
9.815676 |
0.993309 |
1.276800 |
shuffling |
262 |
0.105123 |
0.005581 |
524 |
11048 |
1.643678 |
2.098540 |
5.672902 |
0.189351 |
-0.069373 |
-1.056194 |
-0.057329 |
0.355340 |
0.01 |
gex_nbr_vs_tcr_cluster |
| 97 |
90.789272 |
89.61 |
9.756941 |
0.757410 |
1.143899 |
shuffling |
262 |
0.108160 |
0.006004 |
11848 |
524 |
0.132700 |
-0.676264 |
-1.155820 |
0.597701 |
0.878505 |
0.883814 |
-0.070397 |
0.256193 |
0.01 |
gex_cluster_vs_tcr_nbr |
| 706 |
678.590038 |
678.03 |
32.549487 |
0.859307 |
0.902915 |
shuffling |
262 |
0.091219 |
0.039407 |
6812 |
6812 |
1.125553 |
1.721833 |
3.070619 |
0.259437 |
1.443268 |
3.280935 |
-0.004940 |
0.936571 |
0.10 |
gex_nbr_vs_tcr_nbr |
| 1124 |
1100.567050 |
1097.45 |
41.214652 |
0.644188 |
0.598449 |
shuffling |
262 |
0.115277 |
0.065300 |
6812 |
11048 |
1.125553 |
1.721833 |
3.070619 |
0.189351 |
-0.069373 |
-1.056194 |
-0.019091 |
0.758411 |
0.10 |
gex_nbr_vs_tcr_cluster |
| 1275 |
1180.260536 |
1184.02 |
40.203229 |
2.263002 |
3.659651 |
shuffling |
262 |
0.117067 |
0.070246 |
11848 |
6812 |
0.132700 |
-0.676264 |
-1.155820 |
0.259437 |
1.443268 |
3.280935 |
-0.011697 |
0.850540 |
0.10 |
gex_cluster_vs_tcr_nbr |
graph_vs_graph
Graph vs graph analysis looks for correlation between GEX and TCR space
by finding statistically significant overlap between two similarity graphs,
one defined by GEX similarity and one by TCR sequence similarity.
Overlap is defined one node (clonotype) at a time by looking for overlap
between that node's neighbors in the GEX graph and its neighbors in the
TCR graph. The null model is that the two neighbor sets are chosen
independently at random.
CoNGA looks at two kinds of graphs: K nearest neighbor (KNN) graphs, where
K = neighborhood size is specified as a fraction of the number of
clonotypes (defaults for K are 0.01 and 0.1), and cluster graphs, where
each clonotype is connected to all the other clonotypes in the same
(GEX or TCR) cluster. Overlaps are computed 3 ways (GEX KNN vs TCR KNN,
GEX KNN vs TCR cluster, and GEX cluster vs TCR KNN), for each of the
K values (called nbr_fracs short for neighbor fractions).
Columns (depend slightly on whether hit is KNN v KNN or KNN v cluster):
conga_score = P value for GEX/TCR overlap * number of clonotypes
mait_fraction = fraction of the overlap made up of 'invariant' T cells
num_neighbors* = size of neighborhood (K)
cluster_size = size of cluster (for KNN v cluster graph overlaps)
clone_index = 0-index of clonotype in adata object
| conga_score |
num_neighbors_gex |
num_neighbors_tcr |
overlap |
overlap_corrected |
mait_fraction |
clone_index |
nbr_frac |
graph_overlap_type |
cluster_size |
gex_cluster |
tcr_cluster |
va |
ja |
cdr3a |
vb |
jb |
cdr3b |
| 0.400422 |
26.0 |
26.0 |
8 |
8 |
0.0 |
100 |
0.1 |
gex_nbr_vs_tcr_nbr |
NaN |
3 |
4 |
TRAV19*01 |
TRAJ57*01 |
CALNEGWKGGSEKLVF |
TRBV12-2*01 |
TRBJ1-2*01 |
CASSFTGGSSYDYTF |
| 0.628428 |
26.0 |
NaN |
9 |
9 |
0.0 |
43 |
0.1 |
gex_nbr_vs_tcr_cluster |
34.0 |
1 |
3 |
TRAV13-1*01 |
TRAJ28*01 |
CAAATYSGAGSYQLTF |
TRBV20-1*01 |
TRBJ1-4*01 |
CSATQGGGKLFF |
| 0.693517 |
26.0 |
NaN |
7 |
7 |
0.0 |
209 |
0.1 |
gex_nbr_vs_tcr_cluster |
22.0 |
3 |
4 |
TRAV8-3*01 |
TRAJ11*01 |
CAVSDLGYSTLTF |
TRBV24-1*01 |
TRBJ1-5*01 |
CATSQSRIRQPQYF |
| 0.825420 |
NaN |
26.0 |
12 |
12 |
0.0 |
13 |
0.1 |
gex_cluster_vs_tcr_nbr |
57.0 |
1 |
3 |
TRAV12-1*01 |
TRAJ45*01 |
CAVRLSANRLTF |
TRBV20-1*01 |
TRBJ2-5*01 |
CSALAYRETQYF |
| 0.825420 |
NaN |
26.0 |
12 |
12 |
0.0 |
196 |
0.1 |
gex_cluster_vs_tcr_nbr |
57.0 |
1 |
3 |
TRAV6*01 |
TRAJ18*01 |
CALDMRVRGSTLGKLYF |
TRBV20-1*01 |
TRBJ1-1*01 |
CSADRSGGITEAFF |
| 0.895093 |
NaN |
26.0 |
8 |
8 |
0.0 |
160 |
0.1 |
gex_cluster_vs_tcr_nbr |
29.0 |
3 |
4 |
TRAV38-1*01 |
TRAJ32*01 |
CAFMKHLGGYGGSGNKLIF |
TRBV13*01 |
TRBJ1-2*01 |
CASSPGYRPNYDYTF |
tcr_clumping
This table stores the results of the TCR "clumping"
analysis, which looks for neighborhoods in TCR space with more TCRs than
expected by chance under a simple null model of VDJ rearrangement.
For each TCR in the dataset, we count how many TCRs are within a set of
fixed TCRdist radii (defaults: 24,48,72,96), and compare that number
to the expected number given the size of the dataset using the poisson
model. Inspired by the ALICE and TCRnet methods.
Columns:
clump_type='global' unless we are optionally looking for TCR clumps within
the individual GEX clusters
num_nbrs = neighborhood size (number of other TCRs with TCRdist
tcr_db_match
This table stores significant matches between
TCRs in adata and TCRs in the file /scratch.global/ben_testing/conga/conga/data/new_paired_tcr_db_for_matching_nr.tsv
P values of matches are assigned by turning the raw TCRdist
score into a P value based on a model of the V(D)J rearrangement
process, so matches between TCRs that are very far from germline
(for example) are assigned a higher significance.
Columns:
tcrdist: TCRdist distance between the two TCRs (adata query and db hit)
pvalue_adj: raw P value of the match * num query TCRs * num db TCRs
fdr_value: Benjamini-Hochberg FDR value for match
clone_index: index within adata of the query TCR clonotype
db_index: index of the hit in the database being matched
va,ja,cdr3a,vb,jb,cdr3b
db_XXX: where XXX is a field in the literature database
tcr_graph_vs_gex_features
This table has results from a graph-vs-features analysis in which we
look for genes that are differentially expressed (elevated) in specific
neighborhoods of the TCR neighbor graph. Differential expression is
assessed by a ttest first, for speed, and then
by a mannwhitneyu test for nbrhood/score combinations whose ttest P-value
passes an initial threshold (default is 10* the pvalue threshold).
Each row of the table represents a single significant association, in other
words a neighborhood (defined by the central clonotype index) and a
gene.
The columns are as follows:
ttest_pvalue_adj= ttest_pvalue * number of comparisons
mwu_pvalue_adj= mannwhitney-U P-value * number of comparisons
log2enr = log2 fold change of gene in neighborhood (will be positive)
gex_cluster= the consensus GEX cluster of the clonotypes w/ biased scores
tcr_cluster= the consensus TCR cluster of the clonotypes w/ biased scores
num_fg= the number of clonotypes in the neighborhood (including center)
mean_fg= the mean value of the feature in the neighborhood
mean_bg= the mean value of the feature outside the neighborhood
feature= the name of the gene
mait_fraction= the fraction of the skewed clonotypes that have an invariant
TCR
clone_index= the index in the anndata dataset of the clonotype that is the
center of the neighborhood.
| ttest_pvalue_adj |
mwu_pvalue_adj |
log2enr |
gex_cluster |
tcr_cluster |
feature |
mean_fg |
mean_bg |
num_fg |
clone_index |
mait_fraction |
nbr_frac |
graph_type |
feature_type |
| 2.244313e-17 |
5.018759e-25 |
6.143825 |
1 |
3 |
ENSMMUG00000043894 |
3.022686 |
0.244070 |
35 |
-1 |
0.0 |
0.00 |
tcr_cluster |
gex |
| 7.455134e-03 |
5.542615e-24 |
6.143828 |
0 |
1 |
ENSMMUG00000060662 |
1.944040 |
0.081275 |
27 |
240 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 4.682479e-02 |
4.534282e-21 |
5.903432 |
0 |
1 |
ENSMMUG00000060662 |
1.879571 |
0.088682 |
27 |
238 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.781446e-01 |
6.682292e-19 |
5.722198 |
5 |
1 |
ENSMMUG00000060662 |
1.829304 |
0.094458 |
27 |
243 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.888083e-01 |
1.830371e-18 |
5.641075 |
0 |
1 |
ENSMMUG00000060662 |
1.806370 |
0.097093 |
27 |
230 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.850508e-01 |
2.871732e-18 |
5.587451 |
0 |
1 |
ENSMMUG00000060662 |
1.791071 |
0.098851 |
27 |
225 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.566758e-01 |
4.967101e-18 |
5.475248 |
0 |
1 |
ENSMMUG00000060662 |
1.758713 |
0.102568 |
27 |
228 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.442440e-01 |
5.220053e-18 |
5.483158 |
0 |
1 |
ENSMMUG00000060662 |
1.761009 |
0.102304 |
27 |
219 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.458164e-01 |
6.689329e-18 |
5.454757 |
0 |
1 |
ENSMMUG00000060662 |
1.752754 |
0.103253 |
27 |
223 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.779658e+00 |
6.207490e-16 |
5.277266 |
5 |
1 |
ENSMMUG00000060662 |
1.700546 |
0.109251 |
27 |
227 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.699862e+00 |
1.202008e-15 |
5.223451 |
2 |
1 |
ENSMMUG00000060662 |
1.684516 |
0.111093 |
27 |
234 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.482734e+00 |
1.450578e-15 |
5.281179 |
0 |
1 |
ENSMMUG00000060662 |
1.701708 |
0.109118 |
27 |
239 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.432099e+00 |
1.749898e-15 |
5.251437 |
0 |
1 |
ENSMMUG00000060662 |
1.692864 |
0.110134 |
27 |
224 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.458250e+00 |
2.013772e-15 |
5.250125 |
0 |
1 |
ENSMMUG00000060662 |
1.692473 |
0.110179 |
27 |
237 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.926445e-02 |
4.245694e-14 |
4.892664 |
0 |
1 |
ENSMMUG00000060662 |
1.185828 |
0.073744 |
47 |
-1 |
0.0 |
0.00 |
tcr_cluster |
gex |
| 6.908012e+00 |
5.446651e-13 |
4.922364 |
0 |
1 |
ENSMMUG00000060662 |
1.593302 |
0.121573 |
27 |
218 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 7.862132e+00 |
8.816225e-13 |
4.873058 |
0 |
1 |
ENSMMUG00000060662 |
1.578143 |
0.123315 |
27 |
229 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.255972e-04 |
5.976196e-12 |
5.108541 |
1 |
3 |
ENSMMUG00000043894 |
2.787112 |
0.365727 |
27 |
121 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.189078e-03 |
2.640949e-11 |
4.851444 |
4 |
3 |
ENSMMUG00000043894 |
2.663305 |
0.379952 |
27 |
81 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.735097e-04 |
3.697337e-11 |
4.908379 |
1 |
3 |
ENSMMUG00000043894 |
2.690738 |
0.376800 |
27 |
196 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.475505e-03 |
8.382899e-10 |
4.772083 |
4 |
3 |
ENSMMUG00000043894 |
2.625058 |
0.384346 |
27 |
147 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 6.501781e-03 |
1.058586e-09 |
4.711510 |
2 |
3 |
ENSMMUG00000043894 |
2.595863 |
0.387700 |
27 |
214 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 4.080873e-03 |
1.089854e-09 |
4.775729 |
1 |
3 |
ENSMMUG00000043894 |
2.626815 |
0.384144 |
27 |
18 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.407767e-03 |
1.945689e-09 |
4.730350 |
4 |
3 |
ENSMMUG00000043894 |
2.604943 |
0.386657 |
27 |
24 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.842020e-03 |
2.121496e-09 |
4.723664 |
1 |
3 |
ENSMMUG00000043894 |
2.601721 |
0.387027 |
27 |
118 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.045944e-02 |
3.264041e-09 |
4.555572 |
1 |
3 |
ENSMMUG00000043894 |
2.520710 |
0.396335 |
27 |
184 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 4.371723e-03 |
6.842264e-09 |
4.633070 |
1 |
3 |
ENSMMUG00000043894 |
2.558056 |
0.392044 |
27 |
15 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.164265e+00 |
2.255201e-06 |
4.111250 |
1 |
3 |
ENSMMUG00000043894 |
2.307001 |
0.420889 |
27 |
64 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.079656e+00 |
2.912219e-06 |
4.080762 |
4 |
3 |
ENSMMUG00000043894 |
2.292380 |
0.422569 |
27 |
74 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 4.155404e-01 |
3.661825e-06 |
4.255085 |
1 |
3 |
ENSMMUG00000043894 |
2.376070 |
0.412953 |
27 |
22 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.744567e+00 |
4.961917e-06 |
4.109200 |
1 |
3 |
ENSMMUG00000043894 |
2.306017 |
0.421002 |
27 |
130 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 4.828658e-01 |
6.711579e-06 |
4.175188 |
1 |
3 |
ENSMMUG00000043894 |
2.337686 |
0.417363 |
27 |
110 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.536608e+00 |
8.200559e-06 |
4.010442 |
1 |
3 |
ENSMMUG00000043894 |
2.258687 |
0.426440 |
27 |
68 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 1.888240e+00 |
1.105923e-05 |
4.017658 |
1 |
3 |
ENSMMUG00000043894 |
2.262142 |
0.426043 |
27 |
28 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 5.773776e-01 |
1.317929e-05 |
5.000747 |
2 |
5 |
TRIM23 |
0.780453 |
0.036267 |
3 |
174 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 1.039705e+00 |
3.031310e-05 |
3.988643 |
1 |
3 |
ENSMMUG00000043894 |
2.248252 |
0.427639 |
27 |
79 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 4.565668e+00 |
3.464854e-05 |
4.025198 |
1 |
3 |
ENSMMUG00000043894 |
2.265754 |
0.425628 |
27 |
206 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.560770e-73 |
5.110138e-05 |
5.530760 |
1 |
7 |
ENSMMUG00000056910 |
1.700533 |
0.092432 |
3 |
62 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 7.945207e+00 |
7.666406e-05 |
3.922797 |
1 |
3 |
ENSMMUG00000043894 |
2.216758 |
0.431257 |
27 |
250 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 3.106427e+00 |
1.148110e-04 |
3.982158 |
1 |
3 |
ENSMMUG00000043894 |
2.245148 |
0.427995 |
27 |
119 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 6.064211e+00 |
2.795210e-04 |
3.839704 |
1 |
3 |
ENSMMUG00000043894 |
2.177083 |
0.435816 |
27 |
43 |
0.0 |
0.10 |
tcr_nbr |
gex |
| 2.521144e-28 |
1.952129e-02 |
4.030483 |
4 |
2 |
ZNF48 |
0.569399 |
0.045879 |
3 |
23 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 9.299052e-01 |
2.146723e-02 |
3.877036 |
4 |
4 |
BAG4 |
0.575650 |
0.051615 |
3 |
91 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 1.302097e+00 |
3.562136e-02 |
4.029565 |
0 |
2 |
C13H2orf15 |
0.646091 |
0.054112 |
3 |
21 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 1.668233e-03 |
1.864302e-01 |
6.022600 |
0 |
3 |
ENSMMUG00000060662 |
2.935597 |
0.242402 |
3 |
232 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 6.000005e-05 |
4.352498e-01 |
3.897599 |
2 |
5 |
BRWD3 |
0.780453 |
0.076350 |
3 |
174 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 1.149514e-110 |
4.611845e-01 |
3.790806 |
3 |
4 |
ENSMMUG00000049532 |
0.629644 |
0.061435 |
3 |
94 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 1.239246e-04 |
5.026338e-01 |
3.732104 |
4 |
0 |
AKT1 |
0.592910 |
0.059116 |
3 |
155 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 3.231656e-01 |
7.589127e-01 |
5.612850 |
1 |
1 |
ENSMMUG00000060662 |
2.681532 |
0.245344 |
3 |
219 |
0.0 |
0.01 |
tcr_nbr |
gex |
| 1.487335e-98 |
1.141779e+00 |
3.527302 |
3 |
4 |
CHERP |
0.629644 |
0.073305 |
3 |
94 |
0.0 |
0.01 |
tcr_nbr |
gex |
Omitted 10 lines
tcr_graph_vs_gex_features_plot
This plot summarizes the results of a graph
versus features analysis by labeling the clonotypes at the center of
each biased neighborhood with the name of the feature biased in that
neighborhood. The feature names are drawn in colored boxes whose
color is determined by the strength and direction of the feature score bias
(from bright red for features that are strongly elevated to bright blue
for features that are strongly decreased in the corresponding neighborhoods,
relative to the rest of the dataset).
At most one feature (the top scoring) is shown for each clonotype
(ie, neighborhood). The UMAP xy coordinates for this plot are
stored in adata.obsm['X_tcr_2d']. The score used for ranking correlations
is 'mwu_pvalue_adj'. The threshold score for displaying a feature is
1.0. The feature column is 'feature'. Since
we also run graph-vs-features using "neighbor" graphs that are defined
by clusters, ie where each clonotype is connected to all the other
clonotypes in the same cluster, some biased features may be associated with
a cluster rather than a specific clonotype. Those features are labeled with
a '*' at the end and shown near the centroid of the clonotypes belonging
to that cluster.
Image source: emoryPair8Final_tcr_graph_vs_gex_features_plot.png
tcr_graph_vs_gex_features_panels
Graph-versus-feature analysis was used to identify
a set of GEX features that showed biased distributions
in TCR neighborhoods. This plot shows the distribution of the
top-scoring GEX features on the TCR
UMAP 2D landscape. The features are ranked by 'mwu_pvalue_adj' ie
Mann-Whitney-Wilcoxon adjusted P value (raw P value * number of comparisons).
At most 3 features from clonotype neighbhorhoods
in each (GEX,TCR) cluster pair are shown. The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Points are plotted in order of increasing feature score.
Image source: emoryPair8Final_tcr_graph_vs_gex_features_panels.png
tcr_genes_vs_gex_features
This table has results from a graph-vs-features analysis in which we
look for genes that are differentially expressed (elevated) in specific
neighborhoods of the TCR neighbor graph. Differential expression is
assessed by a ttest first, for speed, and then
by a mannwhitneyu test for nbrhood/score combinations whose ttest P-value
passes an initial threshold (default is 10* the pvalue threshold).
Each row of the table represents a single significant association, in other
words a neighborhood (defined by the central clonotype index) and a
gene.
The columns are as follows:
ttest_pvalue_adj= ttest_pvalue * number of comparisons
mwu_pvalue_adj= mannwhitney-U P-value * number of comparisons
log2enr = log2 fold change of gene in neighborhood (will be positive)
gex_cluster= the consensus GEX cluster of the clonotypes w/ biased scores
tcr_cluster= the consensus TCR cluster of the clonotypes w/ biased scores
num_fg= the number of clonotypes in the neighborhood (including center)
mean_fg= the mean value of the feature in the neighborhood
mean_bg= the mean value of the feature outside the neighborhood
feature= the name of the gene
mait_fraction= the fraction of the skewed clonotypes that have an invariant
TCR
clone_index= the index in the anndata dataset of the clonotype that is the
center of the neighborhood.
In this analysis the TCR graph is defined by
connecting all clonotypes that have the same VA/JA/VB/JB-gene segment
(it's run four times, once with each gene segment type)
| ttest_pvalue_adj |
mwu_pvalue_adj |
log2enr |
gex_cluster |
tcr_cluster |
feature |
mean_fg |
mean_bg |
num_fg |
clone_index |
mait_fraction |
gene_segment |
graph_type |
feature_type |
| 6.269412e-17 |
4.853489e-46 |
9.062205 |
0 |
3 |
ENSMMUG00000060662 |
2.554212 |
0.021946 |
26 |
-1 |
0.0 |
TRAV8-7 |
tcr_genes |
gex |
| 2.999463e-08 |
3.610592e-44 |
10.043410 |
1 |
2 |
ENSMMUG00000062211 |
3.326379 |
0.025114 |
15 |
-1 |
0.0 |
TRBV12-2 |
tcr_genes |
gex |
| 6.511641e-10 |
1.178803e-31 |
8.973724 |
5 |
2 |
ENSMMUG00000062085 |
3.317979 |
0.051564 |
15 |
-1 |
0.0 |
TRBV4-3 |
tcr_genes |
gex |
| 1.779122e-46 |
1.488535e-29 |
6.679359 |
1 |
3 |
ENSMMUG00000043894 |
3.228590 |
0.212323 |
35 |
-1 |
0.0 |
TRBV20-1 |
tcr_genes |
gex |
| 1.868253e+00 |
4.198438e-28 |
10.208363 |
1 |
2 |
ENSMMUG00000063185 |
3.207270 |
0.019844 |
6 |
-1 |
0.0 |
TRBV4-2 |
tcr_genes |
gex |
| 3.882604e+00 |
4.330226e-26 |
7.986221 |
5 |
3 |
ENSMMUG00000059325 |
1.954375 |
0.023616 |
13 |
-1 |
0.0 |
TRAV25 |
tcr_genes |
gex |
| 1.531591e+00 |
1.778148e-11 |
7.778437 |
3 |
5 |
ENSMMUG00000051385 |
3.355458 |
0.118651 |
6 |
-1 |
0.0 |
TRBV7-4 |
tcr_genes |
gex |
| 1.261532e-01 |
3.482693e-09 |
7.808343 |
2 |
0 |
ENSMMUG00000051385 |
3.462733 |
0.129158 |
5 |
-1 |
0.0 |
TRBV7-6 |
tcr_genes |
gex |
| 1.541306e-01 |
2.908451e-05 |
5.660920 |
2 |
1 |
ENSMMUG00000056515 |
3.238345 |
0.394789 |
9 |
-1 |
0.0 |
TRBV6-3 |
tcr_genes |
gex |
| 8.653139e-02 |
5.763194e-02 |
4.572084 |
0 |
6 |
ENSMMUG00000043894 |
2.899598 |
0.543311 |
8 |
-1 |
0.0 |
TRBV21-1 |
tcr_genes |
gex |
| 8.744927e+00 |
6.177033e-02 |
3.117088 |
4 |
4 |
ENSMMUG00000056515 |
1.773075 |
0.446913 |
9 |
-1 |
0.0 |
TRBV10-1 |
tcr_genes |
gex |
| 2.863030e-01 |
1.179343e-01 |
4.100708 |
1 |
7 |
ENSMMUG00000056515 |
2.353249 |
0.441388 |
7 |
-1 |
0.0 |
TRBV9 |
tcr_genes |
gex |
| 2.837480e-01 |
1.199131e-01 |
6.194817 |
5 |
0 |
ENSMMUG00000056515 |
3.698022 |
0.430103 |
5 |
-1 |
0.0 |
TRBV6-2 |
tcr_genes |
gex |
| 2.583847e-12 |
2.701260e+00 |
2.769026 |
2 |
0 |
GPATCH2 |
0.590825 |
0.111690 |
4 |
-1 |
0.0 |
TRAV35 |
tcr_genes |
gex |
| 4.150764e-11 |
8.588965e+00 |
2.750653 |
2 |
0 |
MANBA |
0.590825 |
0.113044 |
4 |
-1 |
0.0 |
TRAV35 |
tcr_genes |
gex |
| 8.748592e-01 |
9.787085e+00 |
1.029846 |
0 |
0 |
MATR3 |
1.264374 |
0.808449 |
24 |
-1 |
0.0 |
TRBJ1-4 |
tcr_genes |
gex |
tcr_genes_vs_gex_features_panels
Graph-versus-feature analysis was used to identify
a set of GEX features that showed biased distributions
in TCR neighborhoods. This plot shows the distribution of the
top-scoring GEX features on the TCR
UMAP 2D landscape. The features are ranked by 'mwu_pvalue_adj' ie
Mann-Whitney-Wilcoxon adjusted P value (raw P value * number of comparisons).
At most 3 features from clonotype neighbhorhoods
in each (GEX,TCR) cluster pair are shown. The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Points are plotted in order of increasing feature score.
Image source: emoryPair8Final_tcr_genes_vs_gex_features_panels.png
gex_graph_vs_tcr_features
This table has results from a graph-vs-features analysis in which we
look at the distribution of a set of TCR-defined features over the GEX
neighbor graph. We look for neighborhoods in the graph that have biased
score distributions, as assessed by a ttest first, for speed, and then
by a mannwhitneyu test for nbrhood/score combinations whose ttest P-value
passes an initial threshold (default is 10* the pvalue threshold).
Each row of the table represents a single significant association, in other
words a neighborhood (defined by the central clonotype index) and a
tcr feature.
The columns are as follows:
ttest_pvalue_adj= ttest_pvalue * number of comparisons
ttest_stat= ttest statistic (sign indicates where feature is up or down)
mwu_pvalue_adj= mannwhitney-U P-value * number of comparisons
gex_cluster= the consensus GEX cluster of the clonotypes w/ biased scores
tcr_cluster= the consensus TCR cluster of the clonotypes w/ biased scores
num_fg= the number of clonotypes in the neighborhood (including center)
mean_fg= the mean value of the feature in the neighborhood
mean_bg= the mean value of the feature outside the neighborhood
feature= the name of the TCR score
mait_fraction= the fraction of the skewed clonotypes that have an invariant
TCR
clone_index= the index in the anndata dataset of the clonotype that is the
center of the neighborhood.
| ttest_pvalue_adj |
ttest_stat |
mwu_pvalue_adj |
gex_cluster |
tcr_cluster |
num_fg |
mean_fg |
mean_bg |
feature |
mait_fraction |
clone_index |
nbr_frac |
graph_type |
feature_type |
| 1.808341e-118 |
44.463843 |
0.149465 |
2.0 |
2.0 |
3.0 |
1.000000 |
0.115830 |
TRBJ2-1 |
0.0 |
33 |
0.01 |
gex_nbr |
tcr |
| 7.525556e-115 |
42.863519 |
0.305571 |
5.0 |
3.0 |
3.0 |
1.000000 |
0.123552 |
TRBV20-1 |
0.0 |
68 |
0.01 |
gex_nbr |
tcr |
| 7.525556e-115 |
42.863519 |
0.305571 |
1.0 |
3.0 |
3.0 |
1.000000 |
0.123552 |
TRBV20-1 |
0.0 |
121 |
0.01 |
gex_nbr |
tcr |
| 7.525556e-115 |
42.863519 |
0.305571 |
4.0 |
3.0 |
3.0 |
1.000000 |
0.123552 |
TRBV20-1 |
0.0 |
242 |
0.01 |
gex_nbr |
tcr |
| 2.572694e-01 |
5.130493 |
1.547852 |
1.0 |
0.0 |
27.0 |
-0.047797 |
-0.307910 |
kf6 |
0.0 |
22 |
0.10 |
gex_nbr |
tcr |
| 2.966857e-01 |
-5.061649 |
2.252206 |
4.0 |
3.0 |
27.0 |
-2.182790 |
-1.198783 |
imhc |
0.0 |
246 |
0.10 |
gex_nbr |
tcr |
gex_graph_vs_tcr_features_plot
This plot summarizes the results of a graph
versus features analysis by labeling the clonotypes at the center of
each biased neighborhood with the name of the feature biased in that
neighborhood. The feature names are drawn in colored boxes whose
color is determined by the strength and direction of the feature score bias
(from bright red for features that are strongly elevated to bright blue
for features that are strongly decreased in the corresponding neighborhoods,
relative to the rest of the dataset).
At most one feature (the top scoring) is shown for each clonotype
(ie, neighborhood). The UMAP xy coordinates for this plot are
stored in adata.obsm['X_gex_2d']. The score used for ranking correlations
is 'mwu_pvalue_adj'. The threshold score for displaying a feature is
1.0. The feature column is 'feature'. Since
we also run graph-vs-features using "neighbor" graphs that are defined
by clusters, ie where each clonotype is connected to all the other
clonotypes in the same cluster, some biased features may be associated with
a cluster rather than a specific clonotype. Those features are labeled with
a '*' at the end and shown near the centroid of the clonotypes belonging
to that cluster.
Image source: emoryPair8Final_gex_graph_vs_tcr_features_plot.png
gex_graph_vs_tcr_features_panels
Image source: emoryPair8Final_gex_graph_vs_tcr_features_panels.png
ERROR -- missing image {pngfile}
graph_vs_features_gex_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
GEX landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_gex' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are GEX clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=26 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie GEX features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the GEX features).
Image source: emoryPair8Final_graph_vs_features_gex_clustermap.png
graph_vs_features_tcr_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
TCR landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_tcr' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are TCR clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=26 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie TCR features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the TCR features).
Image source: emoryPair8Final_graph_vs_features_tcr_clustermap.png
graph_vs_summary
Summary figure for the graph-vs-graph and
graph-vs-features analyses.
Image source: emoryPair8Final_graph_vs_summary.png
gex_clusters_tcrdist_trees
These are TCRdist hierarchical clustering trees
for the GEX clusters (cluster assignments stored in
adata.obs['clusters_gex']). The trees are colored by CoNGA score
with a color score range of 2.62e+00 (blue) to 2.62e-09 (red).
For coloring, CoNGA scores are log-transformed, negated, and square-rooted
(with an offset in there, too, roughly speaking).
Image source: emoryPair8Final_gex_clusters_tcrdist_trees.png
conga_threshold_tcrdist_tree
This is a TCRdist hierarchical clustering tree
for the clonotypes with CoNGA score less than 10.0.
The tree is colored by CoNGA score
with a color score range of 1.00e+01 (blue) to 1.00e-08 (red).
For coloring, CoNGA scores are log-transformed, negated, and square-rooted
(with an offset in there, too, roughly speaking).
Image source: emoryPair8Final_conga_threshold_tcrdist_tree.png
hotspot_features
Find GEX (TCR) features that show a biased
distribution across the TCR (GEX) neighbor graph,
using a simplified version of the Hotspot method
from the Yosef lab.
DeTomaso, D., & Yosef, N. (2021).
"Hotspot identifies informative gene modules across modalities
of single-cell genomics."
Cell Systems, 12(5), 446–456.e9.
PMID:33951459
Columns:
Z: HotSpot Z statistic
pvalue_adj: Raw P value times the number of tests (crude Bonferroni
correction)
nbr_frac: The K NN nbr fraction used for the neighbor graph construction
(nbr_frac = 0.1 means K=0.1*num_clonotypes neighbors)
| Z |
pvalue_adj |
feature |
feature_type |
nbr_frac |
| 31.600037 |
2.721964e-215 |
ENSMMUG00000060662 |
gex |
0.10 |
| 29.992100 |
9.182532e-194 |
ENSMMUG00000043894 |
gex |
0.10 |
| 13.770920 |
2.814559e-39 |
ENSMMUG00000062085 |
gex |
0.10 |
| 13.705246 |
6.971152e-39 |
ENSMMUG00000060662 |
gex |
0.01 |
| 13.146993 |
1.307013e-35 |
ENSMMUG00000043894 |
gex |
0.01 |
| 12.224595 |
1.695591e-30 |
ENSMMUG00000062211 |
gex |
0.10 |
| 11.804036 |
2.745959e-28 |
ENSMMUG00000056910 |
gex |
0.10 |
| 9.669365 |
3.003285e-18 |
ENSMMUG00000059325 |
gex |
0.10 |
| 9.167617 |
3.569391e-16 |
ENSMMUG00000056910 |
gex |
0.01 |
| 8.977690 |
2.040930e-15 |
ENSMMUG00000056515 |
gex |
0.10 |
| 8.938303 |
2.916925e-15 |
ENSMMUG00000013725 |
gex |
0.01 |
| 8.899772 |
4.130520e-15 |
ARHGAP24 |
gex |
0.01 |
| 7.093737 |
9.635035e-09 |
ENSMMUG00000059325 |
gex |
0.01 |
| 6.688777 |
1.661048e-07 |
ENSMMUG00000061119 |
gex |
0.01 |
| 5.886012 |
2.920119e-05 |
NRTN |
gex |
0.01 |
| 5.878370 |
3.058139e-05 |
TNS2 |
gex |
0.01 |
| 5.835053 |
3.969021e-05 |
ENSMMUG00000056783 |
gex |
0.01 |
| 5.720882 |
7.821851e-05 |
GSTO2 |
gex |
0.01 |
| 5.700405 |
8.821984e-05 |
ENSMMUG00000062085 |
gex |
0.01 |
| 5.656015 |
1.143521e-04 |
LKAAEAR1 |
gex |
0.01 |
| 5.259207 |
1.067868e-03 |
C4H6orf132 |
gex |
0.01 |
| 5.148158 |
1.941622e-03 |
ENSMMUG00000061119 |
gex |
0.10 |
| 4.909238 |
6.748512e-03 |
ENSMMUG00000052673 |
gex |
0.01 |
| 4.853287 |
8.962868e-03 |
ENSMMUG00000062211 |
gex |
0.01 |
| 4.805447 |
1.139671e-02 |
MORN4 |
gex |
0.01 |
| 4.794499 |
1.203710e-02 |
FGD4 |
gex |
0.01 |
| 4.753354 |
1.476717e-02 |
ENSMMUG00000063055 |
gex |
0.01 |
| 4.678995 |
2.127831e-02 |
ENSMMUG00000056515 |
gex |
0.01 |
| 3.501573 |
2.937006e-02 |
TRBV19 |
tcr |
0.01 |
| 4.601451 |
3.096756e-02 |
PLCB1 |
gex |
0.01 |
hotspot_gex_umap
HotSpot analysis (Nir Yosef lab, PMID: 33951459)
was used to identify a set of GEX (TCR) features that showed biased
distributions in TCR (GEX) space. This plot shows the distribution of the
top-scoring HotSpot features on the GEX
UMAP 2D landscape. The features are ranked by adjusted P value
(raw P value * number of comparisons). The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Features are filtered based on correlation coefficient to reduce
redundancy: if a feature has a correlation of >= 0.9
(the max_feature_correlation argument to conga.plotting.plot_hotspot_umap)
to a previously plotted feature, that feature is skipped.
Points are plotted in order of increasing feature score
Image source: emoryPair8Final_hotspot_combo_features_0.100_nbrs_gex_plot_umap_nbr_avg.png
hotspot_gex_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
GEX landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_gex' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are GEX clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=26 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie GEX features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the GEX features).
Image source: emoryPair8Final_hotspot_combo_features_0.100_nbrs_gex_plot_clustermap_nbr_avg.png
hotspot_tcr_umap
HotSpot analysis (Nir Yosef lab, PMID: 33951459)
was used to identify a set of GEX (TCR) features that showed biased
distributions in TCR (GEX) space. This plot shows the distribution of the
top-scoring HotSpot features on the TCR
UMAP 2D landscape. The features are ranked by adjusted P value
(raw P value * number of comparisons). The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Features are filtered based on correlation coefficient to reduce
redundancy: if a feature has a correlation of >= 0.9
(the max_feature_correlation argument to conga.plotting.plot_hotspot_umap)
to a previously plotted feature, that feature is skipped.
Points are plotted in order of increasing feature score
Image source: emoryPair8Final_hotspot_combo_features_0.100_nbrs_tcr_plot_umap_nbr_avg.png
hotspot_tcr_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
TCR landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_tcr' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are TCR clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=26 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie TCR features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the TCR features).
Image source: emoryPair8Final_hotspot_combo_features_0.100_nbrs_tcr_plot_clustermap_nbr_avg.png